The 2.1A crystal structure of the far-red fluorescent protein hcred: inherent conformational flexibility of the chromophore

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).

Ligands and binding sites

• CRU · 4-[(4Z)-1-(carboxymethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-4-iminobutanoic acid · ligand · 4 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, D, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–D · 1667 Ų buried · 18 hydrogen bonds · protein-protein
• A–B · 1638 Ų buried · 14 hydrogen bonds · protein-protein
• B–D · 528 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 183 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 38 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

• 1YZW · The 2.1A Crystal Structure of the Far-red Fluorescent Protein HcRed: Inherent… · the same entry in another collection · chain A against A, TM-score 1.00
• Q95W85 · AlphaFold monomer V2.0 prediction for GFP-like non-fluorescent chromoprotein (Q95W85) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q95W85
• Elsewhere: RCSB PDB 1YZW · PDBe 1YZW · UniProt Q95W85